title: Medaka_Control #2

description: Transcriptome profile of a wild type 40 Oryzias latipes (Medaka) embryo wild type, biological rep2


title: Plasma,T1D,S6b

status: Public on May 03 2024

type: SRA

city: Siena

first: Francesco

last: Dotta

state: Si

address: Viale Bracci 16

department: Department of Medicine, surgery and neuroscience

country: Italy

institute: University of Siena

library_source: transcriptomic

data_processing:
Data were analysed using QIAGEN GeneGlobe Data Analysis Center portal. Resulting reads were mapped referring to miRbase v21 and piRNABank using QIAGEN Gene Globe data analysis center software
Assembly: GRCh38/hg38
Supplementary files format and content: semicolon separated value file includes raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: plasma

extract_protocol:
Total RNA extraction was performed from 200 µL of plasma through Serum/Plasma Norgen kit (cat. 55000, Thorold, ON L2V 4Y6, Canada)
Small RNA-derived cDNA libraries were prepared using QiaSeq miRNA library kit (cat. 331505, Qiagen)

tag: tissue

value: plasma


title: KGN, PFOS_1X, P10A

city: Solna

first: Tianyi

last: Li

address: Bioclinicum NKS J5:20, Solnavägen 30

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institute

data_processing:
bcl2fastq (v2.20.0.422) was used to demuliplex the fastq files.
umi_tools extract (v1.0) was then used to extract the barcodes/UMI and add them to the read names in the fastqs
Fastq files were aligned using STAR (v2.7.5b) to the human genome (GRCh38) obtained from Ensembl
The resulted bam files were then deduplicated using umi_tools dedup (v1.0)
Gene counting was then performed using featureCounts (v1.5.1) with Ensembl annotations (Homo_sapiens.GRCh38.101.gtf)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files for all Samples

source_name: ovary

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1 ng of total RNA was used for the construction of sequencing libraries.
Libraries was prepared using QIAseq UPX 3’Transcriptome kit (Qiagen) according to manufacturer's protocol

value: ovary

tag: cell line

value: granulosa cancer cell line KGN

tag: group

tag: genotype

value: WT

tag: concentration


title: Medaka_Control #1

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

description: Transcriptome profile of a wild type 40 Oryzias latipes (Medaka) embryo wild type, biological rep1

data_processing:
Sequence reads were trimmed using bbduk software(https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/usage-guide/) (bbmap suite 37.31) to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6) and then aligned on mm10 reference sequence using STAR
Genome_build: oryLat2
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

organism: Oryzias latipes

source_name: Embryo

growth_protocol: The Cab-strain of medaka fish (Oryzias latipes) was maintained as described in Avellino et al., 2013. Embryos were staged according to the method proposed by Iwamatsu (Iwamatsu, 2004). All studies on fish were conducted in strict accordance with the institutional guidelines for animal research and approved by the Italian Ministry of Health; Department of Public Health, Animal Health, Nutrition and Food Safety in accordance to the law on animal experimentation (D.Lgs. 26/2014). Furthermore, all animal treatments were reviewed and approved in advance by the Ethics Committee at the TIGEM Institute, (Pozzuoli (NA), Italy).

extract_protocol:
RNA was quantified and mixed at 10ng/µl
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaSeq500 (Illumina) with a read length of 100 bp

tag: developmental stage

value: Stage 40

value: embryo

tag: gender

value: not determined


title: VDR ATAC siNfia 1

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

country: Japan

institute: Japanese Foundation for Cancer Research

library_source: genomic

data_processing:
Fastq files were generated by RTA in Illumina NextSeq 550.
Adaptor sequence were trimmed by Skewer
Reads were mapped to mm10 genome by bowtie2
PCR de-duplicate was performed by Picard
Peak call was performed by MACS2
Assembly: mm10
Supplementary files format and content: peak summit data

molecule: genomic DNA

organism: Mus musculus

source_name: cell line

extract_protocol:
To isolate GNP and hyperplasia cells from P7 and P28 Atoh1EGFP cerebella, the tissues were dissociated, followed by percoll gradient centrifugation as previously described. For tumor cell isolation, tumor-bearing cerebella was dissociated with Trypsin/DNase and filtrated though 40 μm cell strainer (CORNING). Subsequently, the cells were suspended in cold DPBS containing 1% BSA for cell sorting of EGFP positive cells with FACSAriaTM sorters (BD Biosciences).
Libraries were prepared with the Omni-ATAC protocol.

value: cell line

value: VDR

tag: cell type

value: medulloblastoma

tag: treatment

value: siNfia 1


title: Plasma,T1D,S6


title: KGN, PFOS_10X, P14A


title: MOD rep3

city: hanzhou

first: Yishan

last: Lv

address: 548 Binwen Road

country: China

institute: Zhejiang Chinese Medical University

data_processing:
The raw paired-end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean data from K. obovata samples was used to do denovo assembly with Trinity (http://trinityrnaseq.sourceforge.net/)
All the assembled transcripts were searched against the (National Center for Biotechnology Information) NCBI protein non-redundant (NR), Clusters of Orthologous Genes (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases using BLASTX to identify the proteins that had the highest sequence similarity with the given transcripts to retrieve their function annotations and a typical cut-off E-values less than 1.0×10−5 was set. Blast2GO software
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: experiment type

extract_protocol:
Total RNA from each sample was extracted using TRIzol® Reagent according to the manufacturer’s instructions (Invitrogen, Carlsbard, CA, USA) and genomic DNA was removed using DNase I (TaKara, Shiga, Japan)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: skin

value: IMQ


title: VDR ATAC siNC 3

value: siNC 3


title: Plasma,T1D,S5


title: MOD rep2


title: Plasma,T1D,S4


title: VDR ATAC siNC 2

value: siNC 2


title: Plasma,T1D,S3


title: MOD rep1


title: VDR ATAC 3


title: CON rep3

source_name: wild type

value: Control


title: KGN, PFOS_100X, P14A


title: KGN, PFOS_10X, P10B


title: CON rep2


title: KGN, PFOS_100X, P11A


title: Plasma,T1D,S2


title: VDR ATAC siNfia 2

value: siNfia 2


title: Plasma,T1D,S1

value: plasma


title: VDR ATAC 1


title: KGN, PFOS_100X, P10A

value: ovary


title: VDR ATAC 2


title: CON rep1


title: KGN, PCB180_1X, P14A

value: granulosa cancer cell line KGN


title: Perio_cont

city: Okayama

first: Shigeki

last: Suzuki

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Operative Dentistry

institute: Okayama University

description: YD92_15: YD92_16

data_processing:
Trim Galore
hisat2
makeTagDirectory
analyzeRepeats.pl rna mm10 -strand both -count exons  -condenseGenes
getDiffExpression.pl
Assembly: mm10
Supplementary files format and content: excel

source_name: periodontal tissue

extract_protocol:
RNA was isolated from diseccted peridontal tissue and liver tissue with RNAiso plus. Purified RNA was DNase-treated and further used for RNA-seq analyses.
Input RNA was converted to cDNA libraries using the NEBNExt poly(A) mRNA magnetic isolation module. Libraries were sequenced using 150-bp paired-end reads on an illumine Novaseq instruments.

treatment_protocol: The mice were anesthetized, and silk ligatures (Elp Sterile Blade Silk, Black, 5–0, Akiyama Medical MFG. CO., LTD, Tokyo, Japan) were tied around their second maxillary molars for 14 days.

value: periodontal tissue

value: wild type


title: Tumor ATAC 3

source_name: primary

value: primary


title: KGN, PCB180_1X, P11B

value: WT


title: KGN, PFOS_10X, P11B


title: 8745_1

city: Nashville

first: Jonathan

middle: A

last: Kropski

state: TN

department: Medicine

country: USA

institute: Vanderbilt University Medical Center

description: 10X 5'v2

library_source: transcriptomic single cell

data_processing:
Cellranger v6.1.2
Genetic demultiplexing - vireo
Doublet calling - scDblFinder
Data integration/annotation -> Scanpy, Harmony, CellTypist
Assembly: GRCh38-2020-A
Supplementary files format and content: cell_sort_cleaned.h5adf:  processed anndata object
Supplementary files format and content: vireo and scDblFinger output to enable genetic demultiplexing for 8745_1
Supplementary files format and content: vireo and scDblFinger output to enable genetic demultiplexing for 8745_2

molecule: polyA RNA

source_name: lung

extract_protocol:
collagenase/dispase digest using Gentlemacs Octo-dissociator
10X 5'v2

value: lung

value: epithelial


title: VDR ATAC siNC 1

value: cell line

value: VDR

value: medulloblastoma

value: siNC 1


title: 8745_2

description: 10X 5'v2


title: Perio_perio

description: YD92_11: YD92_12

value: ligature-induced periodontitis


title: PDX12, PDX, shNFIB, biol rep4

city: Paris

first: Jacob

last: Torrejon Diaz

address: 26 Rue d'Ulm

country: France

institute: Curie Institute

data_processing:
RNAseq v4.0 (Nextflow rna-seq analysis pipeline, Institute Curie)
raw sequencing reads checked for quality with Fastqc and trimmed for adapter sequences
Trimmed reads aligned on the human hg38 (PDXs) and mouse mm10 (VDR cells) reference genomes using the STAR mapper
Generation raw count table per gene and sample
Assembly: hg38 (PDXs KD NFI) / mm10 (VDR KD NFI)
Supplementary files format and content: tab-delimited text file includes raw counts for PDXs KD NFI dataset
Supplementary files format and content: tab-delimited text file includes raw counts for VDR KD NFI dataset

source_name: PDX12 (PDX)

growth_protocol: Tumor cells for PDXs were isolated from PDX tumor chunks with a Percoll gradient. Both murine cell line and PDX cells were cultured and infected in adherent conditions (poly-D-lysine + matrigel precoated dishes). Growth medium for PDX and murine cells consisted of Neurobasal™ Medium (GIBCO) supplemented with 0.45% D+-Glucose (Sigma), 4 mM L-Glutamine (GIBCO), 100 U/mL penicillin/streptomycin (GIBCO), 1X Serum-free supplement B27 (GIBCO).

extract_protocol:
RNeasy Plus Mini Kit (74134, Qiagen)
Stranded mRNA prep Ligation-Illumina

treatment_protocol: Lentiviral infection with shRNAs. Cells were harvested 3 days after infection, the pellets were flash-frozen in liquid nitrogen and kept at -80°C until RNA extraction.

value: PDX12 (PDX)

value: Medulloblastoma


title: Tumor ATAC 1


title: KGN, PCB180_1X, P10A


title: Tumor ATAC 2


title: Liv_cont

description: YD92_7: YD92_8

source_name: liver

value: liver


title: KGN, PCB180_10X, P14A


title: PDX12, PDX, shNFIB, biol rep3


title: PNC ATAC 3

value: hyperplasia


title: KGN, PCB180_10X, P11B

value: ovary


title: PDX12, PDX, shNFIA, biol rep4


title: PNC ATAC 2


title: PDX12, PDX, NC, biol rep4


title: KGN, PCB180_10X, P10A

value: granulosa cancer cell line KGN


title: CRISPRcharm_non-targeting_sgRNA_rep2

city: Cambridge

first: Tessa

last: Bertozzi

state: MA

address: 455 Main St

institute: Whitehead Institute

data_processing:
Reads were aligned to the mouse genome (mm39) using STAR 2.7.1a and quantified using featureCounts 1.6.2.
Assembly: mm39
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

growth_protocol: Neuro-2a ( ATCC, CCL-131) cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 100 units/mL streptomycin, 100 μg/ml penicillin, and 2 mM glutamine, and maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Cells were dislodged from 6-well plates using Trizol and total RNA was extracted using the Direct-zol RNA Miniprep Kit (Zymo, R2051).
Libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche, KK8560)

tag: sgrna


title: CRISPRcharm_non-targeting_sgRNA_rep3


title: KGN, PCB180_100X, P14A


title: PDX12, PDX, shNFIA, biol rep3


title: CRISPRcharm_non-targeting_sgRNA_rep1


title: PNC ATAC 1


title: KGN, PCB180_100X, P11A


title: PDX12, PDX, NC, biol rep3


title: Ptch1GNP ATAC 3

value: granule neuron progenitors


title: Ptch1GNP ATAC 2


title: PDX12, PDX, shNFIB, biol rep2


title: KGN, PCB180_100X, P10A


title: Ptch1GNP ATAC 1


title: PDX12, PDX, shNFIA, biol rep2


title: Liv_perio

description: YD92_3: YD92_4

value: wild type


title: KGN, PCB156_1X, P14A


title: CRISPRcharm_Prnp-targeting_sgRNA_rep1


title: 20220113C-Mt-NFIB-rep3_S2_R1.fastq.gz

data_processing:
Fastq files were generated by RTA in Illumina NextSeq 550.
Adaptor sequence were trimmed by Skewer
Reads were mapped to mm10 genome by bowtie2
Peak call was performed by MACS2
Assembly: mm10
Supplementary files format and content: peak summit data
Library strategy: Cut&Tag

extract_protocol:
GNPs, PNCs and tumor cells were isolated from P7, P28 and adult cerebellum by percoll gradient centrifugation, respectively. These isolated 1 x 105 cells were directly subjected to CUT & Tag library preparation.
CUT & Tag was performed according to the online protocol from EpiCypher

value: primary


title: PDX12, PDX, NC, biol rep2


title: PDX12, PDX, shNFIB, biol rep1


title: 20220113C-Mt-NFIA-rep3_S1_R1.fastq.gz


title: Empty_vector_Prnp-targeting_sgRNA_rep3


title: KGN, PCB156_1X, P11A

value: WT


title: 20220118C-Mt-NFIB-rep2_S7_R1.fastq.gz


title: Empty_vector_Prnp-targeting_sgRNA_rep1


title: KGN, PCB156_10X, P14A


title: 20220118C-Mt-NFIA-rep2_S6_R1.fastq.gz


title: PDX12, PDX, shNFIA, biol rep1


title: Empty_vector_Prnp-targeting_sgRNA_rep2


title: CRISPRcharm_Prnp-targeting_sgRNA_rep3


title: 20211116C-msTumor-NFIB_S8_R1.fastq.gz


title: CRISPRcharm_Prnp-targeting_sgRNA_rep2


title: KGN, PCB156_10X, P10B


title: ZFcharm_Kv1_rep2


title: KGN, PCB156_1X, P10B


title: BT084, PDX, shNFIB, biol rep3

source_name: BT084 (PDX)

value: BT084 (PDX)


title: BT084, PDX, shNFIA, biol rep3


title: 20211201C-Hyperplasia-NFIB_merged_R1.fastq.gz


title: ZFcharm_Kv1_rep1


title: KGN, PCB156_100X, P11B


title: Empty_vector_rep3


title: BT084, PDX, shNFIB, biol rep2


title: KGN, PCB156_100X, P10A


title: 20211201C-Hyperplasia-NFIA_merged_R1.fastq.gz


title: 20211116C-msTumor-NFIA_S7_R1.fastq.gz


title: KGN, PCB156_10X, P11A


title: 20211110C-Hyperplasia-2-NFIB_S11_R1.fastq.gz


title: PDX12, PDX, NC, biol rep1


title: KGN, DDE_1X, P14A


title: Empty_vector_rep1


title: 20211110C-Hyperplasia-2-NFIA_S10_R1.fastq.gz


title: BT084, PDX, NC, biol rep2


title: KGN, DDE_1X, P11A


title: miR379-410 cKO animal 6

city: Zürich

first: Gerhard

last: Schratt

address: Winterthurerstrasse 190

department: D-HEST

country: Switzerland

institute: ETH Zürich

data_processing:
RNAseq quantification was performed using salmon 1.3.0 with the --seqBias option on the GENCODE M20 transcriptome
Assembly: GRCm38
Supplementary files format and content: The `readcount_matrix.tab` provides the read count in each sample and gene.

source_name: Hippocampus (bulk tissue)

extract_protocol:
Trizol-chloroform RNA extraction
NEB Next® Ultra RNA Library Prep Kit

value: Hippocampus (bulk tissue)

value: miR379-410 knockout

tag: Sex

value: Male


title: 20211110C-Hyperplasia-1-NFIB_S8_R1.fastq.gz


title: BT084, PDX, shNFIB, biol rep1


title: KGN, DDE_1X, P10A


title: BT084, PDX, shNFIA, biol rep1


title: miR379-410 cKO animal 5


title: KGN, DDE_10X, P14A


title: BT084, PDX, NC, biol rep3


title: miR379-410 cKO animal 4


title: 20211201C-GNP-NFIB_merged_R1.fastq.gz


title: BT084, PDX, NC, biol rep1


title: Empty_vector_rep2


title: BT084, PDX, shNFIA, biol rep2


title: KGN, DDE_10X, P11A


title: 20211201C-GNP-NFIA_merged_R1.fastq.gz


title: KGN, DDE_10X, P10A


title: miR379-410 cKO animal 3


title: 20211110C-GNP-2-NFIB_S5_R1.fastq.gz


title: PDX meningioma, control, late radiation, rep3

city: San Francisco

first: Abrar

last: Choudhury

state: California

institute: University of California, San Francisco

data_processing:
Library demultiplexing, read alignment to the hg19 and mm10 reference genomes, identification of empty droplets, and UMI quantification was performed using CellRanger v6.1.2
Single cell UMI count data were processed in R v4.2.3 with the Seurat v4.3.0 package. Cells were classified as human or mouse cells based on the percentage of UMIs aligning to each genome, with a threshold of 97% for human cells and a threshole of 75% for mouse cells.
Further processing was done using the sctransform workflow, with scaling based on regression of UMI count and percentage of reads attributed to mitochondrial genes per cell.
Assembly: hg19 and mm10
Supplementary files format and content: Matrix table with the number of unique molecular identifiers for every feature (gene) by row and every barcode (cell) by column
Supplementary files format and content: Sequences corresponding to every barcode in the matrix table
Supplementary files format and content: Sequences corresponding to every feature in the matrix table

source_name: patient-derived xenograft

extract_protocol:
Fresh pdx meningiomas were dissociated into single cells by mincing and then treating with collagenase, trypsin, and RBC lysis buffer. RNA was extracted using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.1.
RNA libraries were prepared for sequencing using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.1.

value: patient-derived xenograft

value: meningioma cells

tag: notch3 expression_status

value: control

tag: radiation

value: late timepoint


title: miR379-410 cKO animal 2


title: KGN, DDE_100X, P14A


title: 20211110C-GNP-2-NFIA_S4_R1.fastq.gz


title: PDX meningioma, control, late radiation, rep2


title: KGN, DDE_100X, P11A


title: 20211110C-Hyperplasia-1-NFIA_S7_R1.fastq.gz


title: PDX meningioma, control, late radiation, rep1


title: miR379-410 cKO animal 1


title: Wild type animal 6

value: Wild type


title: 20211110C-GNP-1-NFIB_S2_R1.fastq.gz


title: PDX meningioma, control, early radiation, rep3

value: early timepoint


title: 20211110C-GNP-1-NFIA_S1_R1.fastq.gz


title: Wild type animal 5


title: KGN, HCB_1X, P14A


title: Wild type animal 4


title: PDX meningioma, control, early radiation, rep2


title: 04_FEB

city: Hamburg

first: Johannes

last: Allweier

address: Bernhard-Nocht-Straße 74

country: Germany

institute: Bernhard Nocht Institute for Tropical Medicine

data_processing:
The RNAseq data were mapped to the human reference genome (GRCh38.109) using CLC Genomics 202 Workbench 21.0 (QIAGEN)
Assembly: GRCh38.109
Supplementary files format and content: ExpressionBroweser as MS-excel file contains gene and transcript expression level counts, normalized expression counts and statistics and differential gene expression between multiple treatment variables.

source_name: Brain microvascular endothelium

growth_protocol: The HBEC-5i cell line (ATCC CRL-3245) was cultured in DMEM/F12 medium supplemented with L-glutamine and sodium bicarbonate (2.438 g/l) at 37°C in 5% CO2. . falciparum isolate IT4 (FCR3S1.2) was cultured in human 0+ erythrocytes at a hematocrit of 5% in 154 the presence of 10% human A+ serum according to standard procedures (Trager and Jensen, 2005). 155 Parasites were synchronized once a week with 5% sorbitol (Lambros and Vanderberg, 1979).

extract_protocol:
Samples were collected in TRIzol (Thermo Fisher Scientific) and isoated using the PureLink RNA Mini Kit (Thermo Fisher Scientific). Removal of possible contamination with gDNA with TURBO DNA-free 194 kit (Fisher Scientific, Thermo Fisher).
Library preparation and subsequent RNA sequencing was performed on an Illumina HiSeq 4000 PE100 platform from BGI (BGI Group).

treatment_protocol: Co-incubation of iRBCs was performed for 7 h in T-25 flasks at either 37°C or 40°C (iRBC-IT4var04-37C or iRBC-IT4var04-40C). HBEC-5i cells cultured at 37°C or 40°C +/- niRBCs (hematocrit 1%) served as controls (Control-37C or niRBCs-37C or  Control-40C)

value: Brain microvascular endothelium

value: HBEC-5i (ATCC CRL-3245)

value: cell line


title: PDX meningioma, control, early radiation, rep1


title: KGN, HCB_1X, P11A

value: ovary

value: granulosa cancer cell line KGN


title: Wild type animal 3


title: PDX meningioma, control, no radiation, rep5


title: Wild type animal 2


title: 02_FEB


title: PDX meningioma, control, no radiation, rep4


title: KGN, HCB_10X, P14A


title: KGN, HCB_10X, P11A


title: 04_RBC_IT4_FEB


title: KGN, HCB_10X, P10A


title: PDX meningioma, control, no radiation, rep3


title: 02_RBC_IT4_FEB


title: KGN, DDE_100X, P10A


title: 01_RBC_IT4_FEB


title: MWA+2DG sample6

city: Nanjing

first: Xinyu

last: Tang

address: 300 Guangzhou Road

institute: The First Affiliated Hospital with Nanjing Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: spleen

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: spleen

value: CD8+T cells


title: PDX meningioma, control, no radiation, rep2


title: PDX meningioma, control, no radiation, rep1


title: KGN, HCB_100X, P14A

value: WT


title: MWA+2DG sample4


title: 04_RBC_IT4


title: PDX meningioma, Notch3 ab, no radiation, rep3

value: inhibitory antibody


title: KGN, HCB_1X, P10A


title: MWA+PBS sample3

value: PBS


title: 02_RBC_IT4


title: 01_FEB


title: PDX meningioma, Notch3 ab, no radiation, rep2


title: MWA+PBS sample2


title: Wild type animal 1

value: Hippocampus (bulk tissue)

value: Male


title: 01_RBC_IT4


title: PDX meningioma, Notch3 ab, no radiation, rep1

value: patient-derived xenograft

value: meningioma cells


title: COV434, DMSO, P35A

value: DMSO


title: MWA+2DG sample5


title: MWA+PBS sample1


title: PDX meningioma, Notch3 OE, late radiation, rep3

value: overexpression

value: late timepoint


title: VDR, cell line, shNFIB, biol rep3

source_name: VDR cells

value: VDR cells

value: Medulloblastoma


title: 02_RBC

value: Brain microvascular endothelium

value: HBEC-5i (ATCC CRL-3245)

value: cell line


title: 04_RBC


title: COV434, DMSO, P29A

value: ovary

value: granulosa cancer cell line KGN


title: PDX meningioma, Notch3 OE, late radiation, rep2


title: VDR, cell line, shNFIA, biol rep3


title: 01_RBC


title: COV434, Untreated, P35A

value: small cell carcinoma cell line COV434

value: WT

value: MEDIA


title: KGN, HCB_100X, P11A


title: 04_Control


title: VDR, cell line, NC, biol rep3


title: KGN, HCB_100X, P10A


title: KGN, PCB156_100X, P14A


title: PDX meningioma, Notch3 OE, early radiation, rep3

value: early timepoint


title: VDR, cell line, shNFIB, biol rep2


title: 02_Control


title: PDX meningioma, Notch3 OE, early radiation, rep2


title: COV434, Untreated, P29A_P4


title: COV434, DMSO, P30A


title: VDR, cell line, NC, biol rep2


title: 01_Control


title: VDR, cell line, shNFIA, biol rep2


title: PDX meningioma, Notch3 OE, early radiation, rep1


title: PDX meningioma, Notch3 OE, late radiation, rep1


title: COV434, MIX_1X, P33A


title: VDR, cell line, shNFIB, biol rep1


title: sci-1-day

city: 南通

first: xing

middle: yi

last: song

state: 江苏

address: 江苏省南通市启秀路19号

department: 神经再生

institute: 南通大学

data_processing:
The Cell Ranger software was obtained from 10x Genomics website   https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
Alignment, filtering,   barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode   matrix and determine clusters.
Dimensionality reduction was performed using PCA and the first ten principle   compoments were used to generate clusters by K-means algorithm and graph-based algorithm, respectively.
Assembly: GRCz11
Supplementary files format and content: Matrix table with raw gene count  for every gene and every sample

organism: Danio rerio

source_name: Wild type zebrafish

extract_protocol:
single cells were suspended in PBS containing 0.04% BSA
According to the manufacture’s introduction, Single-cell RNA-seq libraries were   constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading   strategy

tag: age

value: 4 month


title: PDX meningioma, Notch3 OE, no radiation, rep2

value: patient-derived xenograft


title: COV434, MIX_1X, P28A

source_name: ovary


title: COV434, MIX_1X, P27A


title: sci-7-days

address: 江苏省南通市启秀路19号


title: con

address: 江苏省南通市启秀路19号


title: VDR, cell line, shNFIA, biol rep1


title: COV434, Untreated, P30A


title: PDX meningioma, Notch3 OE, no radiation, rep1

value: meningioma cells


title: PDX meningioma, Notch3 OE, no radiation, rep3


title: COV434, MIX_10X, P33A


title: VDR, cell line, NC, biol rep1


title: COV434, MIX_10X, P28A


title: Control mouse lung

city: Columbus

first: Matthew

last: Cannon

state: Ohio

address: 700 Childrens Drive

department: Center for Childhood Cancer

institute: Nationwide Childrens Hospital

description: Control lung from healthy SCID mouse

data_processing:
BCL files were converted to fastq files with Cellranger mkfastq
Fastq files were processed using Cellranger count
Assembly: mm10 and hg19
Supplementary files format and content: Tar files for each sample include the contents of the filtered_feature_bc_matrix folder output by Cellranger count (barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz)

organism:
Homo sapiens
Mus musculus

extract_protocol:
Tumors harvested from mice were processed using the human tumor dissociation kit (Miltenyi Biotec, 130-095-929) with a GentleMacs Octo Dissociator with Heaters (Miltenyi Biotec, 130-096-427). OS-17 and niche cells expressing slpm-Cherry were isolated using a BD Influx cell sorter using laser 610/20 BP.
Single cell suspensions in 0.04% BSA-PBS of dissociated tumor tissues were generated and run on Chromium Single Cell 3′RNA-sequencing system (10x Genomics) with the Reagent Kit v3.1 (10X Genomics, PN-1000121) according to the manufacturer's instructions. Briefly, cells were loaded into Chromium Next GEM Chip G Single Cell Kit (10x Genomics, PN-1000120) with a targeted cell recovery of 5,000-8,000 cells per sample.

value: lung

tag: sample type

value: control lung


title: ZFcharm_Kv1_rep3


title: HFD, replicated 3, scRNA-seq

city: Xi'an

first: Wenbin

last: Cao

state: Shanxi

address: 76 Yanta West Road, Xi’an, Shaanxi 710061, China

institute: Xi'an Jiaotong University

description:
Sample 3_HFD
10x Genomics

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using an internal pipeline.
Raw reads were processed to generate gene expression Matrix using SCOPE-tools
Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads and the trimmed R2 reads were employed STAR for the alignment of reads against the GRCm38 mouse reference genome.
The reads were localized to the genome, further localized to the genes by utilizing the featureCounts software.
The functions from Seurat was used for dimension-reduction and clustering. Then we used NormalizeData and ScaleData funcitons to normalize and scale all gene expression, and selected the top 2000 variable genes with FindVariableFeautres function for PCA analysis. !Sample_data_processing = Using the top 20 principle components, we separated cells into multiple clusters with FindClusters.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files
the '*update.tar.gz' contains the files processed with CeleScope v1.15.0, while the '.tsv' and '.mtx' files with CeleScope v1.4.0.

source_name: testis

extract_protocol:
The fresh tissues were stored in the sCelLiveTM Tissue Preservation Solution (Singleron) on ice after the surgery within 30 mins. The specimens were washed with Hanks Balanced Salt Solution (HBSS) for three times, minced into small pieces, and then digested with 3 mL sCelLiveTM Tissue Dissociation Solution (Singleron) by Singleron PythoN™ Tissue Dissociation System at 37 °C for 15 min. The cell suspension was collected and filtered through a 40-micron sterile strainer. Afterwards, the GEXSCOPE® red blood cell lysis buﬀer (RCLB, Singleron) was added, and the mixture[Cell: RCLB=1:2 (volume ratio)] was incubated at room temperature for 5-8 min to remove red blood cells. The mixture was then centrifuged at 300 × g 4 ℃ for 5 mins to remove supernatant and suspended softly with PBS
Single-cell suspensions (2×105 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) (Ref). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: testis

tag: strain

value: ICR

value: male

value: high-fat diet (HFD)


title: COV434, MIX_10X, P27A


title: Mouse 4, pooled barcoded tissue Tregs, FB

first: Adrian

last: Liston

address: Tennis Court Road

department: Department of Pathology

country: United Kingdom

institute: University of Cambridge

description: 10X Genomics

library_source: other

data_processing:
The demultiplexing, barcode processing, gene counting, VDJ assembly and aggregation were performed in Cell Ranger
For TCR sequence analysis, scRNA data was used to allow for paired TCRαβ chain identification. Row sequencing data was processed with CellRanger 5.0.0 without barcode mismatches allowed and with multi-features analysis (gene expression, vdj-t, totalseq hashtags). Features were linked based on cell barcodes and tissue origin was retrieved based on hashtags signals when highest hashtag count was at least 30 times higher than the others using a custom R script. Gene expression and TCR repertoire analysis were generated in R using circlize, dplyr, ggplot2, ggsci, Matrix, pheatmap,scales, scater, Seurat, SingleCellExperiment, tidyr, viridis packages. For repertoire analysis, a TCR clonotype is associated to a unique set of Trav, tra_cdr3, trbv, trb_cdr3. The custom script is available at: https://github.com/AdrianListon/TissueTregTCR.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-Seq

molecule: protein

source_name: Blood, liver, kidney, pancreas, small intestine

extract_protocol:
Tregs were flow sorted on a BD Influx, Aria, Jazz or Fusion on the basis of CD4+Foxp3Thy1.1+ i.v.CD45- CD19-CD11b-CD8-F4/80-. Cells were labeled with Hashtag TotalSeq regents and loaded onto the 10x Chromium Controller. Sequencing was performed on an Illumina HiSeq.
scRNA-Seq was performed using 10x Genomics 5’ VDJ Single Cell Immune Profiling.

value: Treg

tag: animal id

value: Mouse 4

tag: library type

value: HTO


title: AD, LINGO2shRNA, biol rep 3

city: New York

first: Gunnar

last: Hargus

state: NY

address: 650W 168th Street

department: Pathology and Cell Biology

institute: Columbia University

description:
bulk RNA seq
lingo2kd_processed_files.csv
ADkd3

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
We perform a pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Human:GRCh38.p12; Mouse:GRCm38.p6) using kallisto (0.44.0).
We test for differentially expressed genes under various conditions using Sleuth or DESeq2, R packages designed to test differential expression between two experimental groups from RNA-seq counts data.
Assembly: Human:GRCh38.p12
Supplementary files format and content: estimated counts values for each gene (computed from tximport R package)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
We use poly-A pull-down to enrich mRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry.

tag: cell line

value: iPSC-derived neurons


title: AD, LINGO2shRNA, biol rep 2

description:
bulk RNA seq
lingo2kd_processed_files.csv
ADkd2


title: Mouse 4, pooled barcoded tissue Tregs, VDJ

description: 10X Genomics

tag: tissue

value: Blood, liver, kidney, pancreas, small intestine

value: VDJ


title: COV434, MIX_100X, P33A

first: Tianyi

last: Li

institute: Karolinska Institute

data_processing:
bcl2fastq (v2.20.0.422) was used to demuliplex the fastq files.
umi_tools extract (v1.0) was then used to extract the barcodes/UMI and add them to the read names in the fastqs
Fastq files were aligned using STAR (v2.7.5b) to the human genome (GRCh38) obtained from Ensembl
The resulted bam files were then deduplicated using umi_tools dedup (v1.0)
Gene counting was then performed using featureCounts (v1.5.1) with Ensembl annotations (Homo_sapiens.GRCh38.101.gtf)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files for all Samples

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1 ng of total RNA was used for the construction of sequencing libraries.
Libraries was prepared using QIAseq UPX 3’Transcriptome kit (Qiagen) according to manufacturer's protocol

value: ovary

value: small cell carcinoma cell line COV434

tag: group

tag: genotype

value: WT


title: HFD, replicated 1, scRNA-seq

description:
Sample 1_HFD
10x Genomics


title: AD, LINGO2shRNA, biol rep 1

description:
bulk RNA seq
lingo2kd_processed_files.csv
ADkd1


title: Mouse 4, pooled barcoded tissue Tregs, GEX

description: 10X Genomics

value: mRNA


title: CD, replicated 3, scRNA-seq

description:
Sample 3_CD
10x Genomics

value: conventional diet (CD)


title: COV434, MIX_100X, P27A_P4

tag: concentration


title: COV434, MIX_100X, P28A


title: Mouse 3, pooled barcoded tissue Tregs, FB

description: 10X Genomics

value: Mouse 3


title: Mouse 3, pooled barcoded tissue Tregs, VDJ

description: 10X Genomics


title: AD, empty vecto, biol rep 3

description:
bulk RNA seq
lingo2kd_processed_files.csv
AD3


title: CD, replicated 2, scRNA-seq

description:
Sample 2_CD
10x Genomics


title: AD, empty vecto, biol rep 2

description:
bulk RNA seq
lingo2kd_processed_files.csv
AD2


title: Primary, HCB_10X, patient3

value: Primary ovarian cells


title: COV434, MIX_100X, P27A_P3


title: Mouse 3, pooled barcoded tissue Tregs, GEX

description: 10X Genomics


title: COV434, MIX_100X, P27A_P2


title: AD, empty vecto, biol rep 1

description:
bulk RNA seq
lingo2kd_processed_files.csv
AD1


title: CD, replicated 1, scRNA-seq

description:
Sample 1_CD
10x Genomics

value: testis


title: Mouse 2, pooled barcoded tissue Tregs, FB

description: 10X Genomics

value: Mouse 2


title: COV434, PFOS_1X, P33A


title: Plasma_treat4h_1

city: Chuncheon

first: Sehyun

last: Chae

address: 1 Kangwondaehakgil

department: Division of Chemical Engineering and Bioengineering

country: South Korea

institute: Kangwon National University

data_processing:
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling.
Illumina adapter sequences were removed using the Flexbar software (version 3.5.0), and the remaining reads sequences were aligned to the mouse genome (GRCm38) using Tophat2 software (version 2.1.1) with the default parameters.
After the alignment, the numbers of reads mapped to the gene features (GTF file of GRCm38.91) were counted using HTseq sofrware. The read counts for the samples in each condition were then normalized using the TMM (trimmed mean of M-values) normalization of the edgeR package.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include TMM-normalized read counts for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: B16 melanoma cells

extract_protocol:
Total RNA was extracted from B16 melanoma cells. The integrity of total RNA was analyzed using the 2100 Bioanalyzer instrument of Agilent Technologies. The RNA integrity number (RIN) values for all samples were > 8. Poly(A) mRNA isolation from total RNA and fragmentation was conducted using the Illumina TruSeq Stranded mRNA Prep Kit (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: B16 melanoma cells

value: exosome-mimetic nanovesicles (EMs)-treated plasma


title: Plasma_treat4h_2


title: control, empty vector, biol rep 3

description:
bulk RNA seq
lingo2kd_processed_files.csv
Ctrl3


title: HFD, replicated 2, scRNA-seq

description:
Sample 2_HFD
10x Genomics

value: ICR

value: male

value: high-fat diet (HFD)


title: COV434, PFOS_1X, P28A

city: Solna


title: Control_2

value: Control


title: Mouse 2, pooled barcoded tissue Tregs, VDJ

description: 10X Genomics

value: Blood, liver, kidney, pancreas, small intestine

value: Treg


title: control, empty vector, biol rep 1

description:
bulk RNA seq
lingo2kd_processed_files.csv
Ctrl1

value: iPSC-derived neurons


title: control, empty vector, biol rep 2

description:
bulk RNA seq
lingo2kd_processed_files.csv
Ctrl2


title: Mouse 2, pooled barcoded tissue Tregs, GEX

description: 10X Genomics


title: Mouse 1, pooled barcoded tissue Tregs, FB

description: 10X Genomics

value: Mouse 1

value: HTO


title: COV434, PFOS_10X, P33A

value: ovary

value: small cell carcinoma cell line COV434

value: WT


title: COV434, PFOS_1X, P27A


title: AD, clone2, biol rep 3

description:
bulk RNA seq
in_vitro_processed_file.csv
vitro_bulk_AD6


title: COV434, PFOS_10X, P28A


title: Control_1


title: AD, clone2, biol rep 1

description:
bulk RNA seq
in_vitro_processed_file.csv
vitro_bulk_AD4


title: COV434, PFOS_10X, P27A


title: Mouse 1, pooled barcoded tissue Tregs, GEX

description: 10X Genomics

value: mRNA


title: GVHD mouse dosed with anti-CX3CL1 mAb (1 mg/head) [ID_1544]

city: Tsukuba

first: Yoshimasa

last: Sakamoto

state: Ibaraki

address: 5-1-3 Tokodai

institute: Eisai Co Ltd.

data_processing:
All raw sequencing reads were trimmed using Trimmomatic software.
Bases and QC assessment of sequencing were generated using FastQC.
QC‐passed reads were aligned to the Ensembl GRCm38.88 reference genome using Star v2.5.2b.
The abundance of transcripts was then estimated using an Expectation‐Maximization algorithm implemented in the software package RSEM v1.2.31 (https://github.com/deweylab/RSEM/).
Assembly: Ensembl GRCm38.88
Supplementary files format and content: experiment_580_analysis_1255.genes.fpkm_tracking.xlsx: Excel file includes TPM values for each Sample.

source_name: skin

extract_protocol:
Total RNA was isolated from the mouse skin using RNeasy spin columns (Qiagen) and digested with DNase I (Qiagen) to remove chromosomal DNA.
The preparation of the mRNA-Seq library was carried out using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) in accordance with the manufacturer’s instructions optimized to Illumina Multiplexed Sequencing (https://targetepigenomics.org/docs/library_construction_protocol_perlab/Biswal_RNAseq_TruSeq.pdf).

value: skin

tag: mouse model

value: GVHD

value: anti-CX3CL1 mAb (1 mg/head)


title: Arabidopsis, mPing only

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description: arabidopsis mPing only

data_processing:
To identify and characterize reads that have both mPing and other regions of the genome, the 3’ adapter was trimmed from raw reads using cutadapt (parameters: -a "ATCACTAGTGAATTCGCGGCC;min_overlap=10;e=0.1" -q 10). Next, only reads containing mPing sequence were identified and the matching mPing sequence was trimmed from the 5’ end using cutadapt (parameters: -g "EXPECTEDMPINGSEQUENCE;min_overlap=35;e=0.1" -q 10).
To remove reads that show mPing at its donor location, these 5’ and 3’ trimmed sequences were mapped to the reference mPing donor sequence using default parameters of bowtie2 with the additional parameter to store donor-unmapped reads (--un). These donor-unmapped reads were then mapped to the genome using default parameters of bowtie2. The start position of each mapping read was collected as the mPing insertion site into the genome.
Assembly: TAIR10 for Arabidopsis and Williams 82 reference genome (Wm82.a4.v1) from Phytozome for soybean.
Supplementary files format and content: A tab-delimited file showing the start site of each read supporting a genomic insertion site is supplied as a processed file. The four columns are chromosome, start site, strand, and sequence of the read.

organism: Arabidopsis thaliana

source_name: 7 day old seedlings

growth_protocol: Arabidopsis thaliana: All plants were grown at 22℃ under 16-hour day conditions in a MTPS-120 growth chamber with 200 µmol m−2 s−1 light intensity.  Glycine max: Plants are grown in the chamber under the following conditions. Temperature: 25°C day/ 23°C night (77°F/73°F); Humidity: 50%; Light: 14-hour day at 200-600 μmol. Regenerated transgenic plants were then transplanted into a greenhouse to mature with following conditions. Temperature: 25°C day/ 23°C night (77°F/73°F); Humidity: 35% minimum; Light: The supplemental lights come on when the sunlight is below 400 W/m²between 6am-8pm (14 hours) from September through May and between 6-10am May through September; Shading: The shade curtain automatically closes to 50% when the sunlight level is over 900 W/m² and it pulls to 100% when the sunlight is over 1000 W/m².

extract_protocol:
High molecular weight DNA was isolated from fresh Arabidopsis seedlings and Soybean leaf tissue using the NucleoBond HMW DNA kit (Takara), and digested by restriction enzymes XbaⅠ and AluⅠ.
Fragmented DNAs ranging from ~450bp to ~2kb were purified from agarose gels, A-tailed by Klenow Fragment (3’-5’ exo-; NEB), and ligated to the pGEM T- Easy vector (Promega). 1 µL of this ligation product was used as a template for primary PCR, followed by secondary PCR using nested primers. mPing specific primers were used with the pGEM T- Easy vector primers for primary and secondary PCRs. Barcoded sequencing adapters were added to the amplicons through their inclusion in the PCR primers. The sequencing library for soybean was constructed similarly, except that the genomic DNA was isolated from leaf tissue and digested by XbaⅠ, PmlⅠ, and AluⅠ.
After passing quality controls, libraries were run on a MiSeq (Illumina) with V2 output (1X300)

treatment_protocol: Arabidopsis thaliana: Various binary vectors were introduced into Agrobacterium tumefaciens GV3101. All transgenic lines were transformed using the Agrobacterium-mediated floral dip method and subsequent selection for Hygromycin-resistant plants.  Glycine max: Various binary vectors were introduced into Agrobacterium tumefaciens AGL1. Mature half-seeds of Soybean (Glycine max var. Williams 82) were transformed to generate transgenic plants using a modified version of the method adapted from a previous publication (PMID: 25300848). Transgenic plants were selected for Basta-resistance and confirmed by PCR.

value: 7 day old seedlings

value: Wt + specific transgenes

tag: ecotype /_cultivar

value: Columbia


title: AD, clone1, biol rep 3

description:
bulk RNA seq
in_vitro_processed_file.csv
vitro_bulk_AD3

tag: cell type


title: COV434, PFOS_100X, P33A

address: Bioclinicum NKS J5:20, Solnavägen 30


title: GVHD mouse dosed with anti-CX3CL1 mAb (1 mg/head) [ID_1546]

tag: treatment


title: AD, clone1, biol rep 2

description:
bulk RNA seq
in_vitro_processed_file.csv
vitro_bulk_AD2


title: COV434, PFOS_100X, P28A


title: GVHD mouse dosed with anti-CX3CL1 mAb (1 mg/head) [ID_1542]


title: Arabidopsis, +ORF1, +ORF2, +Cas9, replicate 3

description: arabidopsis pds3 unfused 3


title: GVHD mouse dosed with anti-CX3CL1 mAb (1 mg/head) [ID_1545]


title: GVHD mouse dosed with anti-CX3CL1 mAb (1 mg/head) [ID_1543]


title: GVHD mouse dosed with anti-CX3CL1 mAb (0.5 mg/head) [ID_1541]

value: anti-CX3CL1 mAb (0.5 mg/head)


title: COV434, PFOS_100X, P27A


title: AD, clone1, biol rep 1

description:
bulk RNA seq
in_vitro_processed_file.csv
vitro_bulk_AD1


title: COV434, PCB180_1X, P33A


title: Mouse 1, pooled barcoded tissue Tregs, VDJ

description: 10X Genomics

value: VDJ


title: AD, clone2, biol rep 2

description:
bulk RNA seq
in_vitro_processed_file.csv
vitro_bulk_AD5


title: control, biol rep 3

description:
bulk RNA seq
in_vitro_processed_file.csv
vitro_bulk_Ctrl3


title: Arabidopsis, +ORF1, +ORF2, +Cas9, replicate 1

description: arabidopsis pds3 unfused 1


title: control, biol rep 2

description:
bulk RNA seq
in_vitro_processed_file.csv
vitro_bulk_Ctrl2


title: Arabidopsis, +ORF1, +ORF2, -Cas9, replicate 2

data_processing:
To identify and characterize reads that have both mPing and other regions of the genome, the 3’ adapter was trimmed from raw reads using cutadapt (parameters: -a "ATCACTAGTGAATTCGCGGCC;min_overlap=10;e=0.1" -q 10). Next, only reads containing mPing sequence were identified and the matching mPing sequence was trimmed from the 5’ end using cutadapt (parameters: -g "EXPECTEDMPINGSEQUENCE;min_overlap=35;e=0.1" -q 10).
To remove reads that show mPing at its donor location, these 5’ and 3’ trimmed sequences were mapped to the reference mPing donor sequence using default parameters of bowtie2 with the additional parameter to store donor-unmapped reads (--un). These donor-unmapped reads were then mapped to the genome using default parameters of bowtie2. The start position of each mapping read was collected as the mPing insertion site into the genome.
Assembly: TAIR10 for Arabidopsis and Williams 82 reference genome (Wm82.a4.v1) from Phytozome for soybean.
Supplementary files format and content: A tab-delimited file showing the start site of each read supporting a genomic insertion site is supplied as a processed file. The four columns are chromosome, start site, strand, and sequence of the read.
Library strategy: DNA-seq

growth_protocol: Arabidopsis thaliana: All plants were grown at 22℃ under 16-hour day conditions in a MTPS-120 growth chamber with 200 µmol m−2 s−1 light intensity.    Glycine max: Plants are grown in the chamber under the following conditions. Temperature: 25°C day/ 23°C night (77°F/73°F); Humidity: 50%; Light: 14-hour day at 200-600 μmol. Regenerated transgenic plants were then transplanted into a greenhouse to mature with following conditions. Temperature: 25°C day/ 23°C night (77°F/73°F); Humidity: 35% minimum; Light: The supplemental lights come on when the sunlight is below 400 W/m²between 6am-8pm (14 hours) from September through May and between 6-10am May through September; Shading: The shade curtain automatically closes to 50% when the sunlight level is over 900 W/m² and it pulls to 100% when the sunlight is over 1000 W/m².

extract_protocol:
High molecular weight DNA was isolated from fresh Arabidopsis seedlings and Soybean leaf tissue using the NucleoBond HMW DNA kit (Takara), and digested by restriction enzymes XbaⅠ and AluⅠ.
Fragmented DNAs ranging from ~450bp to ~2kb were purified from agarose gels, A-tailed by Klenow Fragment (3’-5’ exo-; NEB), and ligated to the pGEM T- Easy vector (Promega). 1 µL of this ligation product was used as a template for primary PCR, followed by secondary PCR using nested primers. mPing specific primers were used with the pGEM T- Easy vector primers for primary and secondary PCRs.  Barcoded sequencing adapters were added to the amplicons through their inclusion in the PCR primers. The sequencing library for soybean was constructed similarly, except that the genomic DNA was isolated from leaf tissue and digested by XbaⅠ, PmlⅠ, and AluⅠ.
After passing quality controls, libraries were run on a MiSeq (Illumina) with V2 output (1X300)

treatment_protocol: Arabidopsis thaliana: Various binary vectors were introduced into Agrobacterium tumefaciens GV3101. All transgenic lines were transformed using the Agrobacterium-mediated floral dip method and subsequent selection for Hygromycin-resistant plants.    Glycine max: Various binary vectors were introduced into Agrobacterium tumefaciens AGL1. Mature half-seeds of Soybean (Glycine max var. Williams 82) were transformed to generate transgenic plants using a modified version of the method adapted from a previous publication (PMID: 25300848). Transgenic plants were selected for Basta-resistance and confirmed by PCR.

tag: cultivar


title: COV434, PCB180_1X, P28A


title: control, biol rep 1

description:
bulk RNA seq
in_vitro_processed_file.csv
vitro_bulk_Ctrl1


title: Arabidopsis, +ORF1, +ORF2-Cas9, replicate 3

description: arabidopsis pds3 3


title: GVHD mouse dosed with control IgG [ID_1538]

value: control IgG


title: AD graft; clone 2; biol rep3

description:
single nuclei RNAseq
CTRLs_APPs_HUMAN_re_merge_3rd_NEURON_ASTRO_2_month.reproc_no_prefix.count_matrix.csv
CTRLs_APPs_HUMAN_re_merge_3rd_NEURON_ASTRO_2_month.reproc_no_prefix.meta_data.csv
CTRLs_APPs_MOUSE_re_merge_2_month.reproc_no_prefix.count_matrix.csv
CTRLs_APPs_MOUSE_re_merge_2_month.reproc_no_prefix.meta_data.csv

data_processing:
The 10x genomics' cellranger software version 5.0.1 was used to process the data
Assembly: Human: GRCh38; mouse: mm10
Supplementary files format and content: comma separated text files include absolute gene counts for each single nucleus and accompanying sample meta data.

source_name: Micro-dissected graft

extract_protocol:
Frozen grafts were homogenized using a Dounce homogenizer in a tissue homogenizing buffer that contains 30% sucrose and 0.1% Triton-X 100. 15 strokes with the loss pestle followed by 15 strokes with the tight pestle were applied to each graft. The brain lysate was then mixed well using P1000 pipette followed by filtration through 35 μm nylon mesh (Corning; 352235) followed by 10 min centrifugation of 1000g at 4°C. The pellet was resuspended in homogenizing buffer and filtered through 35 μm nylon mesh again followed by 10 min centrifugation of 1000g at 4°C. The pellet was resuspended in PBS supplemented with 1% BSA and a RNAase inhibitor (Invitrogen; SUPERaseIN; AM2696).
Chromium Controller (10x Genomics) was used and single Cell 3’ Reagent Kit v2 or v3 (Chromium Single Cell 3’ Library & Gel Bead Kit v2, catalog number: 120237; Chromium Single Cell A Chip Kit, 48 runs, catalog number: 120236; 10x Genomics) was used. Illumina NOVAseq 6000 platformV4 with 150bp paired end reads was applied for the sequencing step.

value: Micro-dissected graft


title: GVHD mouse dosed with anti-CX3CL1 mAb (0.5 mg/head) [ID_1539]


title: COV434, PCB180_10X, P33A


title: GVHD mouse dosed with control IgG [ID_1537]


title: Arabidopsis, +ORF1, +ORF2, -Cas9, replicate 1


title: GVHD mouse dosed with control IgG [ID_1535]


title: AD graft; clone 2; biol rep2


title: Arabidopsis, Wt Col


title: COV434, PCB180_10X, P28A


title: Arabidopsis, +ORF1, +ORF2-Cas9, replicate 2


title: Arabidopsis, +ORF1, +ORF2, +Cas9, replicate 2

description: arabidopsis pds3 unfused 2


title: AD graft; clone 2; biol rep1


title: COV434, PCB180_10X, P27A


title: syngenic mouse dosed with anti-CX3CL1 mAb [ID_1534]

value: syngenic

value: anti-CX3CL1 mAb


title: AD graft; clone 1; biol rep3


title: Arabidopsis, +ORF1, +ORF2-Cas9, replicate 1


title: U+R, +ORF1, +ORF2, +Cas9

data_processing:
3’ adapter sequences were removed using cutadapt (parameters: -a CTGTCTCTTATACACATCT -m 10). These data were used for three different purposes: 1) Determining the insertion site precision, 2) Determining the intactness of the cargo and 3) Determining the junctions of the transposon for investigating seamless insertion. The detailed processing steps for these three investigations is provided in the manuscript.
Assembly: Custom sequences based on targeted insertion locus were used to map the reads. These sequences are provided in the manuscript.
Supplementary files format and content: A tab-delimited file with the read count of each read is provided as a processed file for each sample. These reads can be used to replicate any of the downstream analyses mentioned in the manuscript.
Library strategy: Amplicon-seq

source_name: 10 day old whole seedlings

growth_protocol: All plants were grown at 22℃ under 16-hour day conditions in a MTPS-120 growth chamber with 200 µmol m−2 s−1 light intensity.

extract_protocol:
Genomic DNA was isolated from frozen Arabidopsis seedlings.
PCR amplicons were generated using the primers shown in the manuscript. Sequencing libraries were constructed from the PCR amplicons using the Nextera DNA Flex kit (Illumina) and Hackflex protocol (PMID: 35014949), as described in PMID: 34750500.
After quality control, the library with pooled amplicons was sequenced SE300 on an Illumina MiSeq.

treatment_protocol: Various binary vectors were introduced into Agrobacterium tumefaciens GV3101. All transgenic lines were transformed using the Agrobacterium-mediated floral dip method and subsequent selection for Hygromycin-resistant plants.

value: 10 day old whole seedlings

value: Wild type + corresponding transgenes

tag: ecotype


title: GVHD mouse dosed with anti-CX3CL1 mAb (0.5 mg/head) [ID_1540]


title: AD graft; clone 1; biol rep2


title: syngenic mouse dosed with anti-CX3CL1 mAb [ID_1533]


title: syngenic mouse dosed with anti-CX3CL1 mAb [ID_1532]


title: COV434, PCB180_100X, P33A

value: ovary

value: small cell carcinoma cell line COV434


title: COV434, PCB180_1X, P27A

value: WT


title: U+L, +ORF1, +ORF2, +Cas9


title: COV434, PCB180_100X, P27A


title: AD graft; clone 1; biol rep1


title: syngenic mouse dosed with anti-CX3CL1 mAb [ID_1530]

value: skin


title: COV434, PCB156_1X, P33A


title: Ctrl graft; biol rep 6


title: D+L, +ORF1, +ORF2, +Cas9


title: Ctrl graft; biol rep 5


title: Human meningioma, patient 10

data_processing:
Library demultiplexing, read alignment to the GRCh38 human reference genome, identification of empty droplets, and UMI quantification was performed using CellRanger v6.1.2
Single cell UMI count data were processed in R v4.2.3 with the Seurat v4.3.0 package using the sctransform workflow, with scaling based on regression of UMI count and percentage of reads attributed to mitochondrial genes per cell.
Assembly: GRCh38
Supplementary files format and content: Matrix table with the number of unique molecular identifiers for every feature (gene) by row and every barcode (cell) by column
Supplementary files format and content: Sequences corresponding to every barcode in the matrix table
Supplementary files format and content: Sequences corresponding to every feature in the matrix table

source_name: meningioma

extract_protocol:
A fresh human meningioma was dissociated into single cells by mincing and then treating with collagenase, trypsin, and RBC lysis buffer. RNA was extracted using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.
RNA libraries were prepared for sequencing using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.

value: meningioma


title: syngenic mouse dosed with control IgG [ID_1529]


title: COV434, PCB156_1X, P28A


title: U+R, +ORF1, +ORF2-Cas9


title: syngenic mouse dosed with control IgG [ID_1528]


title: U+L, +ORF1, +ORF2-Cas9


title: COV434, PCB156_1X, P27A


title: Ctrl graft; biol rep 3


title: COV434, PCB156_10X, P33A


title: syngenic mouse dosed with control IgG [ID_1527]


title: Ctrl graft; biol rep 2


title: COV434, PCB156_10X, P28A


title: COV434, PCB180_100X, P28A


title: MWA+2DG 5

source_name: lymph node

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: lymph node


title: D+L, +ORF1, +ORF2-Cas9


title: COV434, PCB156_10X, P27A


title: Ctrl graft; biol rep 1


title: D+R, +ORF1, +ORF2, +Cas9


title: D+R, +ORF1, +ORF2-Cas9


title: MWA+2DG 4


title: polCA (Multiplexing Capture)

city: wien

first: Camilla

last: Bosone

state: Austria

address: Dr Bohr gasse 3

country: Austria

institute: IMBA

description: Cell Multiplexing Oligos

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger (multi) software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/multi)
Assembly: hg38
Supplementary files format and content: Cellranger multi matrix, features and barcode tables

source_name: Human embryonic stem cells (hESC) H9 obtained from WiCell

growth_protocol: Organoids were generated with a modified version of what previously described (Lancaster and Knoblich, 2014; Lancaster et al., 2013). Briefly, on D0 hESCs and iPSCs  were treated with accutase to single cell suspention and transferred to an ultra-low binding 96-well plate (9000 cells/well) for rOrgs, or to a PMDS mould (5,5x106 cells/mould) for eOrgs. Cells aggregated into embrioyd bodies in mTeSR1 supplemented with 50 µM Rho-associated protein kinase (ROCK) inhibitor. PMDS moulds have been sterilized with autoclaving and gamma irradiation, then treated with Pluronic F127 (Sigma-Aldrich P2443) 1% in PBS and wash with PBS several times prior to usage. From D1 on, the medium was replaced daily with Neural Induction Medium (NI) containing DMEM-F12 supplemented with 1X N2 supplement, 1ug/ml heparin solution, 1X GlutaMAX, 1X MEM-NEAA and 50 µM ROCK inhibitor. On D7, embryoid bodies were embedded into droplets of Matrigel and transferred into 6-cm dishes containing Imp-A Medium consisting of 50% DMEM-F12, 50% Neurobasal medium, 1X N2, 1X B27 – Vitamin A, 2.5 g/ml Insulin, 0.05mM BME, 1X GlutaMAX, 1X MEM-NEAA and 1X Antibiotic-Antimycotic (Thermo Fisher 15240062). On D15, media was replaced with Imp+A Medium consisting of 50% DMEM-F12, 50% Neurobasal medium, 1X N2, 1X B27, 2.5 µg /ml Insulin, 0.05mM BME, 1X GlutaMAX, 1X MEM-NEAA, 1X Antibiotic-Antimycotic and organoids were moved to on an orbital shaker under 52 rpm rotating speed. The medium was changed every 2-3 days. From D30 onwards, organoids were fed with Imp+A Medium supplemented with 1% (v/v) matrigel basement membrane, BDNF (20 ng/ml) and GDNF (20 ng/ml)

extract_protocol:
All the polCAs and control (conCAs) have been manually dissected at a stereomicroscope and processed for RNA extraction. For bulk RNAseq, samples were lysed in 350 µl of RLT buffer supplemented with βmercaptoehtanol and RNA was extracted using the RNeasy Micro Kit (Qiagen 74004) following the manufacturer’s protocol. For scRNAseq, manually dissected at a stereomicroscope and processed for dissociation with gentleMACSTM Dissociator in Trypsin/Accutase solution with TURBO™ DNase (Thermo AM2238, 2 U/µL). After dissociation, DPBS-/- + 10% FBS has been gradually added to stop reaction. Samples have been then centrifuged at 400G for 5min at 4ºC and supernatant was aspirated without touching the pellet. The pellet has been resuspended in additional  500µl of DPBS-/- + 10% FBS, filtered through FACS tubes and stained for viability dye DRAQ7 (Biostatus, DR70250, 0.3mM). Live cells have been sorted with a BD FACS Aria™ III on Alexa 700 filter and barcoded with unique CMOs for MULTI-seq analysis.
For scRNAseq, sequencing have been performed on a 10X NovaSeq S4 PE150 XP (single/half lane) platform according to manufacturer’s indications.

treatment_protocol: Fusion with organizer EB at D3 where specified

tag: cmo

value: polaroid1_proximal,CMO301  polaroid1_medial,CMO302  polaroid1_distal,CMO303  polaroid2_proximal,CMO304  polaroid2_medial,CMO305  polaroid2_distal,CMO306  polaroid3_proximal,CMO307  polaroid3_medial,CMO308  polaroid3_distal,CMO309

value: wild-type

value: POLARIZED WITH 1%FGF8 ORGANIZER EB (OrEB)


title: COV434, PCB156_100X, P33A


title: polCA (Gene Expression)

description: polyA RNA

value: Human embryonic stem cells (hESC) H9 obtained from WiCell


title: H9FF polCA7_distal (batch with mutant samples of GSE175592)

data_processing:
Basecalling: RTA 1.18.66.3
Adapter have been clipped with trimgalore (v0.5.0)
Abundant sequences (iGenomes hg38) are removed with bowtie2 (v2.3.4.1).
Cleaned reads are aligned against the genome (GRCh38) with STAR (v2.6.0c).
Reads are counted towards their corresponding gene (ENSEMBL v94) with featureCounts (v1.6.2).
Assembly: GRCh38
Supplementary files format and content: feature count output file (tab-separated; last column contains counts)

extract_protocol:
All the polCAs and control (conCAs) have been manually dissected at a stereomicroscope and processed for RNA extraction. For bulk RNAseq, samples were lysed in 350 µl of RLT buffer supplemented with βmercaptoehtanol and RNA was extracted using the RNeasy Micro Kit (Qiagen 74004) following the manufacturer’s protocol. For scRNAseq, manually dissected at a stereomicroscope and processed for dissociation with gentleMACSTM Dissociator in Trypsin/Accutase solution with TURBO™ DNase (Thermo AM2238, 2 U/µL). After dissociation, DPBS-/- + 10% FBS has been gradually added to stop reaction. Samples have been then centrifuged at 400G for 5min at 4ºC and supernatant was aspirated without touching the pellet. The pellet has been resuspended in additional  500µl of DPBS-/- + 10% FBS, filtered through FACS tubes and stained for viability dye DRAQ7 (Biostatus, DR70250, 0.3mM). Live cells have been sorted with a BD FACS Aria™ III on Alexa 700 filter and barcoded with unique CMOs for MULTI-seq analysis.
For bulk RNAseq, we then assessed RNA concentration and quality with an RNA 6000 Nano Chip (Agilent Technologies) and enriched for mRNA with NEBNext Poly(A) mRNA Magnetic Isolation Module; barcoded samples were then multiplexed and sequenced 50 bp single-end on a HiSeq 2500 (Illumina). mRNA sample enrichment, library preparation, and sequencing were performed by the VBCF NGS Unit (https://www.vbcf.ac.at).


title: H9FF polCA7_medial (batch with mutant samples of GSE175592)


title: COV434, PCB156_100X, P28A


title: Ctrl graft; biol rep 4


title: MWA+2DG 2


title: MWA+2DG 3


title: H9FF polCA7_proximal (batch with mutant samples of GSE175592)


title: MWA+2DG 1


title: control (Multiplexing Capture)

description: Cell Multiplexing Oligos

value: control1_piece1,CMO301  control1_piece2,CMO302  control1_piece3,CMO303  control2_piece1,CMO304  control2_piece2,CMO305  control2_piece3,CMO306  control3_piece1,CMO307  control3_piece2,CMO308  control3_piece3,CMO309

value: UNTREATED


title: COV434, DDE_1X, P33A


title: control (Gene Expression)

description: polyA RNA


title: MWA 5

value: MWA


title: MUTANT DISTAL3 (DMUT3)

description: CD76KANXX_2_15-01-2021_140949_GGTACTTAGTGAGCCA

data_processing:
Basecalling RTA VN:1.18.66.3
Adapter have been clipped with trimgalore (v0.5.0)
Abundant sequences (iGenomes hg38) are removed with bowtie2 (v2.3.4.1).
Cleaned reads are aligned against the genome (GRCh38) with STAR (v2.6.0c).
Reads are counted towards their corresponding gene (ENSEMBL v94) with featureCounts (v1.6.2).
Genome_build: GRCh38
Supplementary_files_format_and_content: feature count output file (tab-separated; last column contains counts)

source_name: D60 MUTANT POLAROID 3

growth_protocol: Organoids were generated with a modified version of what previously described (Lancaster and Knoblich, 2014; Lancaster et al., 2013). Briefly, on D0 hESCs and iPSCs  were treated with accutase to single cell suspention and transferred to an ultra-low binding 96-well plate (9000 cells/well) for rOrgs, or to a PMDS mould (5,5x106 cells/mould) for eOrgs. Cells aggregated into embrioyd bodies in mTeSR1 supplemented with 50 µM Rho-associated protein kinase (ROCK) inhibitor. PMDS moulds have been sterilized with autoclaving and gamma irradiation, then treated with Pluronic F127 (Sigma-Aldrich P2443) 1% in PBS and wash with PBS several times prior to usage. From D1 on, the medium was replaced daily with Neural Induction Medium (NI) containing DMEM-F12 supplemented with 1X N2 supplement, 1 µ/ml heparin solution, 1X GlutaMAX, 1X MEM-NEAA and 50 µM ROCK inhibitor. On D7, embryoid bodies were embedded into droplets of Matrigel and transferred into 6-cm dishes containing Imp-A Medium consisting of 50% DMEM-F12, 50% Neurobasal medium, 1X N2, 1X B27 – Vitamin A, 2.5 µ/ml Insulin, 0.05mM BME, 1X GlutaMAX, 1X MEM-NEAA and 1X Antibiotic-Antimycotic (Thermo Fisher 15240062). On D15, media was replaced with Imp+A Medium consisting of 50% DMEM-F12, 50% Neurobasal medium, 1X N2, 1X B27, 2.5 µg /ml Insulin, 0.05mM BME, 1X GlutaMAX, 1X MEM-NEAA, 1X Antibiotic-Antimycotic and organoids were moved to on an orbital shaker under 52 rpm rotating speed. The medium was changed every 2-3 days. From D30 onwards, organoids were fed with Imp+A Medium supplemented with 1% (v/v) matrigel basement membrane, BDNF (20 ng/ml) and GDNF (20 ng/ml)

extract_protocol:
Three independent PolarOids and one eORG without OrEB (control, C1-3) have been manually dissected at a stereomicroscope and processed for RNA extraction. Samples were lysed in 350 µl of RLT buffer supplemented with βmercaptoehtanol and RNA was extracted using the RNeasy Micro Kit (Qiagen 74004) following the manufacturer’s protocol.
We then assessed RNA concentration and quality with an RNA 6000 Nano Chip (Agilent Technologies) and enriched for mRNA with NEBNext Poly(A) mRNA Magnetic Isolation Module; barcoded samples were then multiplexed and sequenced 50 bp single-end on a HiSeq 2500 (Illumina). mRNA sample enrichment, library preparation, and sequencing were performed by the VBCF NGS Unit (https://www.vbcf.ac.at).

value: Human embryonic stem cells (hESC) H9; FGFR3 380G>A substitution


title: MUTANT MEDIAL3 (MMUT)

description: CD76KANXX_2_15-01-2021_140948_AACGTACGAGGATTAG


title: COV434, DDE_1X, P28A


title: PC_SR_23

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

data_processing:
the reads were trimmed toremove adapter sequences and low-quality ends and reads mapping to contaminating  sequences (e.g., ribosomal RNA, phIX control) were filtered-out.
Genome_build: Hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: Melanoma biopsy

extract_protocol:
RNA was quantified and mixed at 10ng/µl
For RNA-seq analysis, libraries were prepared according to manufacturer's instructions (QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen GmbH) starting from 250ng of total RNA.
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaSeq6000 (Illumina) with a read length of 100 bp

value: BRAFi+MEKi

tag: time

value: Before the starting of 1 cycle

value: Melanoma biopsy

tag: gender

value: not collected


title: MUTANT PROXIMAL3 (PMUT3)

description: CD76KANXX_2_15-01-2021_140947_GCGAGTTAGAGCGGTT


title: COV434, DDE_1X, P27A

value: ovary

value: small cell carcinoma cell line COV434


title: MWA 3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample


title: PC_SR_22


title: MWA 4


title: MUTANT DISTAL2 (DMUT2)

description: CD76KANXX_2_15-01-2021_140946_ACCGCATATAGGTGCT

source_name: D60 MUTANT POLAROID 2


title: COV434, DDE_10X, P33A

value: WT


title: MUTANT MEDIAL2 (MMUT2)

description: CD76KANXX_2_15-01-2021_140945_GTGATGAGGGTGGCAC


title: PC_SR_20


title: MUTANT PROXIMAL2 (PMUT2)

description: CD76KANXX_2_15-01-2021_140944_CAACGCTAGTGTGAAC


title: MWA 1


title: MWA 2


title: PC_SR_19


title: PC_SR_21


title: COV434, PCB156_100X, P27A


title: PC_SR_18


title: COV434, DDE_10X, P28A


title: RNA_Vav1Kmt2d_MUT_CD8SP_Biol rep2

city: Cincinnati

first: Sarah

middle: J

last: Potter

address: 240 Albert Sabin Way, S6.540, MLC 7028

department: Allergy and Immunology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Before processing, the files from each lane were merged. Data were processed using Scientific data Analysis Platform, https://scidap.com using the RNA-Seq pipeline available at (https://github.com/datirium/workflows/workflows/trim-rnaseq-pe.cwl). Briefly, the merged FASTQ files trimmed the adapters and aligned samples to the mouse genome (Mus Musculus [mm10] genome reference consortium mouse build 38, strain: C57BL/6J. 2012/01/09). Genome indices using STAR v2.5.3a (03/17/2017) were generated. Each set of data (Kmt2dSET-fl/fl Cre+) with their corresponding littermate controls (Kmt2dSET-fl/fl) were processed using: A) differential gene expression analysis based on the negative binomial distribution (DESeq2) analysis pipeline (https://github.com/datirium/workflows/workflows/deseq.cwl). DESeq2 runs (i.e., 1. CD4+SP Lck-CreMar, 2. CD8+SP Lck-CreMar, 3. CD8+SP Vav1-iCre) were then exported and filtered in Microsoft Excel based on the following criteria: Log2 Fold Change ≥ 0.59; adjusted p-value ≤ 0.1, RPKM ≥ 5 in at least one condition; or B) RPKM was exported using Feature Expression Merge pipeline (https://github.com/datirium/workflows/workflows/feature-merge.cwl) from each individual sample and graphed in Graphpad Prism.
Assembly: mm10

source_name: Thymocyte

growth_protocol: Mice were sacrificed as Adults

extract_protocol:
RNA was isolated following the manufacturer’s instructions of the Monarch RNA Isolation Kit (New England Biolabs; #T2010S). RIN scores and concentration were performed using High Sensitivity RNA ScreenTape (Agilent Technologies; #5067-5579/#5190-6507) and run using the Agilent Technology software with an electronic ladder. Quality RIN scores above 7 were used for RNA-Seq library preparation.
Library creation was perfromed using KAPA Library Quantification Kit for Illumina (KAPA; #KK4824). Quality checks on size and concentration of libraries was performd using the High Sensitivity D1000 DNA Kit on BioAnalyzer (Agilent; #5067-4626/#5190-6502). Paired-end 50-bp reads were obtained for pooled libraries using Illumina Novaseq 6000.

value: Thymocyte

value: CD8SP Thymocyte

value: Vav1-iCre+; Kmt2dflfl (Kmt2d Knockout)


title: MUTANT MEDIAL1 (MMUT1)

description: CD76KANXX_2_15-01-2021_140942_ATCGGCTACCAATACT

source_name: D60 MUTANT POLAROID 1


title: RNA_Vav1Kmt2d_MUT_CD8SP_Biol rep3


title: COV434, DDE_10X, P27A


title: MUTANT PROXIMAL1 (PMUT1)

description: CD76KANXX_2_15-01-2021_140941_TCTATGTACAGGCATA


title: COV434, DDE_100X, P33A


title: CONTROL3 (CTRL3)

description: CE0J3ANXX_3_09-10-2019_100751_AGCTTCGAGCACTGAG

source_name: D60 ELONGATED ORGANOID (eOrg) CONTROL


title: COV434, DDE_100X, P27A

source_name: ovary


title: PC_SR_13

value: BRAFi

value: At progression assessment


title: RNA_Vav1Kmt2d_WT_CD8SP_Biol rep3

value: Vav1-iCre-; Kmt2dflfl (Littermate Control)


title: PC_SR_14


title: RNA_Vav1Kmt2d_WT_CD8SP_Biol rep2


title: COV434, HCB_1X, P33B


title: RNA_Vav1Kmt2d_MUT_CD8SP_Biol rep1


title: PC_SR_12


title: CONTROL2 (CTRL2)

description: CE0J3ANXX_3_09-10-2019_100750_GATAATCGGAGTTGAT

value: Human embryonic stem cells (hESC) H9 obtained from WiCell


title: RNA_Vav1Kmt2d_WT_CD8SP_Biol rep1


title: MUTANT DISTAL1 (DMUT1)

description: CD76KANXX_2_15-01-2021_140943_GTGGATCGTCGCGCAT

value: POLARIZED WITH 1%FGF8 ORGANIZER EB (OrEB)


title: COV434, HCB_1X, P27B


title: COV434, HCB_1X, P28B


title: PC_SR_11


title: RNA_LckKmt2d_MUT_CD8SP_Biol rep3

value: Lck-CreMar+; Kmt2dflfl (Kmt2d-Knockout)


title: DISTAL3 (D3)

description: CE0J3ANXX_3_09-10-2019_100748_ACATCCGACTGCGGAT

source_name: D60 POLAROID 3


title: CONTROL1 (CTRL1)

description: CE0J3ANXX_3_09-10-2019_100749_CCGGCTCGGCGGCTTG

value: UNTREATED


title: COV434, DDE_100X, P28A


title: PC_SR_17

value: BRAFi+MEKi


title: PC_SR_9


title: COV434, HCB_10X, P33A


title: MEDIAL3 (M3)

description: CE0J3ANXX_3_09-10-2019_100747_ACAGCGACTTATATCA


title: PC_SR_5

value: Before the starting of 1 cycle


title: RNA_LckKmt2d_MUT_CD8SP_Biol rep2


title: RNA_LckKmt2d_MUT_CD8SP_Biol rep1


title: COV434, HCB_10X, P27A


title: DISTAL2 (D2)

description: CE0J3ANXX_3_09-10-2019_100745_CTTACCGACTAACTCA

source_name: D60 POLAROID 2


title: RNA_LckKmt2d_WT_CD8SP_Biol rep3

value: Lck-CreMar-; Kmt2dflfl (Control Littermate)


title: COV434, HCB_100X, P33A


title: PC_SR_4

value: Melanoma biopsy

value: not collected


title: RNA_LckKmt2d_WT_CD8SP_Biol rep2


title: PC_SR_3


title: COV434, HCB_100X, P28A

value: ovary

value: small cell carcinoma cell line COV434


title: RNA_LckKmt2d_WT_CD8SP_Biol rep1

value: Thymocyte


title: PROXIMAL2 (P2)

description: CE0J3ANXX_3_09-10-2019_100743_ATCGTGAGCTTACGGC


title: COV434, HCB_100X, P27B

value: WT


title: PC_SR_1


title: A375_DAB200 #3

description: SmallTranscriptome profile of A375 treated with DABRAFENIB (200nM), biological rep3

data_processing:
We compared the miRNA expression profiles between the A375 and A375-BIR cells   in both control (DMSO) and treatment group by using EdgeR package   (https://www.bioconductor.org/packages/release/bioc/html/edgeR.html) under software   R (version 4.0.2). MiRNAs that have very low counts across all the libraries were re-  moved prior to perform normalization by trimmed mean of M values (TMM)
Genome_build: Reads were aligned and   assigned to Human ENSEMBLE transcripts and genes (hg38 reference) by using RSEM   version 1.2.25 with standard parameters.
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: Melanoma cell line A375

growth_protocol: RPMI 10%FBS, splitting every 48-72h at confluency

extract_protocol:
RNA was quantified and mixed at 10ng/µl
Total RNA (250 ng) from each sample was prepared using Small RNA-Seq Library Prep Kit (Lexogen, GmbH), according to manufacturer's instructions
The library product were  cleaned-up and concentrated with gel-based purification protocol. This step removes  linker-linker artefacts (120 bp) and long library fragments (>200bp) . The sequencing step was performed with NGS  technologies using Illumina Novaseq 6000 SP kit (100 cycles) produced by Illumina.

treatment_protocol: cells has been treated with dabrafenib at concetration of 200nM for 48h and with DMSO (0.1%)

value: DAB


title: RNA_LckKmt2d_MUT_CD4SP_Biol rep3

value: CD4SP Thymocyte


title: DISTAL1 (D1)

description: CE0J3ANXX_3_09-10-2019_100742_CGCTTCTTGTAGATAA

source_name: D60 POLAROID 1 outlier


title: MEDIAL1 (M1)

description: CE0J3ANXX_3_09-10-2019_100741_GGTGCCGACCAACGTC


title: Canine dura, patient 3

data_processing:
Library demultiplexing, read alignment to the ROS_Cfam_1.0 canine reference genome, identification of empty droplets, and UMI quantification was performed using CellRanger v6.1.2
Single cell UMI count data were processed in R v4.2.3 with the Seurat v4.3.0 package using the sctransform workflow, with scaling based on regression of UMI count and percentage of reads attributed to mitochondrial genes per cell.
Assembly: ROS_Cfam_1.0
Supplementary files format and content: matrix.mtx.gz: Matrix table with the number of unique molecular identifiers for every feature (gene) by row and every barcode (cell) by column
Supplementary files format and content: barcodes.tsv.gz: Sequences corresponding to every barcode in the matrix table
Supplementary files format and content: features.tsv.gz: Sequences corresponding to every feature in the matrix table

organism: Canis lupus familiaris

source_name: dura

extract_protocol:
Fresh canine meningiomas were dissociated into single cells by mincing and then treating with collagenase, trypsin, and RBC lysis buffer. RNA was extracted using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.
RNA libraries were prepared for sequencing using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.

value: dura

tag: subject number


title: Canine meningioma, patient 4

value: meningioma


title: COV434, HCB_10X, P28A


title: RNA_LckKmt2d_MUT_CD4SP_Biol rep1


title: PROXIMAL1 (P1)

description: CE0J3ANXX_3_09-10-2019_100740_TTCATAAGGCCAATGT

value: Human embryonic stem cells (hESC) H9 obtained from WiCell


title: A375_DAB200 #2

description: SmallTranscriptome profile of A375 treated with DABRAFENIB (200nM), biological rep2


title: syngenic mouse dosed with anti-CX3CL1 mAb [ID_1531]

source_name: skin

value: skin

value: syngenic

value: anti-CX3CL1 mAb


title: Canine meningioma, patient 3


title: A375_DAB200 #1

description: SmallTranscriptome profile of A375 treated with DABRAFENIB (200nM), biological rep1


title: PC_SR_6

value: BRAFi


title: PROXIMAL3 (P3)

description: CE0J3ANXX_3_09-10-2019_100746_TGTATCTTAATATCTG

value: POLARIZED WITH 1%FGF8 ORGANIZER EB (OrEB)


title: RNA_LckKmt2d_WT_CD4SP_Biol rep3

value: Lck-CreMar-; Kmt2dflfl (Control Littermate)


title: MEDIAL2 (M2)

description: CE0J3ANXX_3_09-10-2019_100744_TCGACCGACCAAGTGC


title: A375_DMSO #_Crt_3

description: SmallTranscriptome profile of A375 treated with DMSO (0.1%), biological rep3

value: DMSO


title: RNA_LckKmt2d_WT_CD4SP_Biol rep2


title: Lung, yak rep2, scRNAseq

city: Chengdu

first: Daoliang

last: Lan

state: Sichuan

address: #16, South Section, 1st Ring Road

institute: Southwest Minzu University

description: 10× Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0.
Assembly: ARS-UCD1.2
Supplementary files format and content: Tab-separated values files and matrix files.

organism: Bos grunniens

source_name: lung

extract_protocol:
Following aseptic procedures, for each individual, lung tissue samples of 1 cm³ in size were precisely collected using surgical scissors from 6 sampling points on both sides of the lung lobes (i.e. left anterior, left middle, left posterior, right anterior, right middle and right posterior lobes), located 5 cm from the lung apex, avoiding bronchial tubes and blood vessels as much as possible. Immediately, each piece of lung tissue was transferred separately to a freezing tube containing cell freezing medium (90% FBS and 10% DMSO) and thoroughly resuspended. For each animal, lung tissue samples collected from 6 different sites were pooled for subsequent single-cell transcriptomic analysis. Lung tissues in cryovials were thawed in a 37 °C water bath and washed 3 times in RPMI 1640 medium. The lung tissues were finely minced into approximately 0.5 mm³ fragments by using sterile surgical scissors in RPMI 1640 medium. These fragments were digested at 37 °C for 30 min in 1 mg/mL Type I collagenase, followed by 10 min of digestion at 37 °C in 0.25% trypsin-EDTA. Lastly, 10% foetal bovine serum was added to stop digestion. Lung tissue suspensions were filtered through a 40 μm cell strainer, and erythrocytes were removed with red blood cell lysis buffer. Lung cells were resuspended in DPBS containing 2% foetal bovine serum, and the cell suspension was counted and stored for subsequent scRNA-seq.
Library was performed according to the manufacter's instructions (single cell 3' v3 protocol, 10× Genomics). In brief, the whole library construction process was divided into 3 steps: GEM Generation & Barcoding, Post GEM-RT Cleanup & cDNA Amplification and 3' Gene Expression Library Construction.

value: lung


title: Lung, yak rep3, scRNAseq

description: 10× Genomics


title: Canine dura, patient 2


title: Canine meningioma, patient 2

source_name: meningioma


title: A375_DMSO #_Crt_2

description: SmallTranscriptome profile of A375 treated with DMSO (0.1%), biological rep2


title: Lung, yak rep1, scRNAseq

description: 10× Genomics


title: RNA_LckKmt2d_WT_CD4SP_Biol rep1


title: A375_BIR_DAB200 #3

description: SmallTranscriptome profile of A375-BIR treated with DABRAFENIB (200nM), biological rep3

source_name: Melanoma cell line A375-BRAF INHIBITOR RESISTANT (BIR)


title: Pool_ko, biological rep3

data_processing:
Sequence reads were trimmed using bbduk software(https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/usage-guide/) (bbmap suite 37.31) to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6) and then aligned on mm10 reference sequence using STAR
Genome_build: oryLat2
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: Stage 40 Oryzias latipes (Medaka)

extract_protocol:
Extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).
Total RNA (500 ng) from each sample was prepared using TruSeq RNA sample prep reagents (Illumina, San Diego, CA, USA) according to manufacturer's instructions

treatment_protocol: No treatment was performed

tag: Stage

value: Stage 40

value: not determined

tag: genotype/variation

value: KO for SEDL

value: embryo


title: Day 49 OS17 met

description: OS17 metastases collected at day 49

data_processing:
BCL files were converted to fastq files with Cellranger mkfastq
Fastq files were processed using Cellranger count
Assembly: mm10 and hg19
Supplementary files format and content: Tar files for each sample include the contents of the filtered_feature_bc_matrix folder output by Cellranger count (barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz)

extract_protocol:
Tumors harvested from mice were processed using the human tumor dissociation kit (Miltenyi Biotec, 130-095-929) with a GentleMacs Octo Dissociator with Heaters (Miltenyi Biotec, 130-096-427). OS-17 and niche cells expressing slpm-Cherry were isolated using a BD Influx cell sorter using laser 610/20 BP.
Single cell suspensions in 0.04% BSA-PBS of dissociated tumor tissues were generated and run on Chromium Single Cell 3′RNA-sequencing system (10x Genomics) with the Reagent Kit v3.1 (10X Genomics, PN-1000121) according to the manufacturer's instructions. Briefly, cells were loaded into Chromium Next GEM Chip G Single Cell Kit (10x Genomics, PN-1000120) with a targeted cell recovery of 5,000-8,000 cells per sample.

tag: cell line

value: OS17 osteosarcoma

tag: time point

value: Day 49

tag: sample type

value: metastasis


title: Differentiated Brown adipocyte, Rotenone Day 7, Rep3

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

institute: Soochow University

data_processing:
RNA-seq reads were aligned to reference genome mm10 with TopHat2 and quantified to the mouse transcriptome (genes) with GFOLD.
Assembly: mm10
Supplementary files format and content: Processed files include read counts for each simple are in tab-delimited text format.

source_name: Immotalized pre brown adipocyte

growth_protocol: Immortalized primary brown preadipocytes were maintained in DMEM (HyClone) supplemented with 10% FBS, 200 units/ml penicillin, and 50 µg/mL streptomycin. Preadipocytes were grown to confluence, and differentiation was induced by incubation in growth medium supplemented with 20 nM insulin, 1 nM 3,3′,5-triiodo-L-thyronine (T3), 0.5 mM methylisobutylxanthine (IBMX), 500 nM dexamethasone and 0.125 mM indomethacin for 3 days. The cells were then cultured in growth medium supplemented with 20 nM insulin and 1 nM T3 for four more days until the cells were fully differentiated.

extract_protocol:
Total RNA were extracted using Trizol reagenet according to the manufactural protocol
Libraries were prepared according to Illumina's instructions accompanying the NEBNext Ultra RNA library Prep Kit for Illumina and purified using Beckman agencourt AMPure XP beads. Library were analyzed using agilent bioanalyzer 2100. The purified DNA was captured using TruSeq PE Cluster kit V4 for cluster generation. Libraries were sequenced on the  Illumina HiSeq X Ten machine following the manufacturer's protocols.

treatment_protocol: On day 7 of differentiation, mature brown adipocyte were treated with 100 nM ROT or DMSO for 16 hours.

value: Immotalized pre brown adipocyte

value: Rotenone treated O/N


title: RNA_LckKmt2d_MUT_CD4SP_Biol rep2

tag: tissue

value: Thymocyte

value: CD4SP Thymocyte

tag: genotype

value: Lck-CreMar+; Kmt2dflfl (Kmt2d-Knockout)


title: Primary tibia OS17

description: OS17 primary tumor from tibia

source_name: tibia

value: tibia

value: primary


title: Pool_ko, biological rep2


title: Differentiated Brown adipocyte, Rotenone Day 7, Rep2


title: Day 28 OS17 met

description: OS17 metastases collected at day 28

value: Day 28


title: Differentiated Brown adipocyte, Rotenone Day 7, Rep1


title: A375_BIR_DAB200 #1

description: SmallTranscriptome profile of A375-BIR treated with DABRAFENIB (200nM), biological rep1

value: DAB


title: A375_BIR_DAB200 #2

description: SmallTranscriptome profile of A375-BIR treated with DABRAFENIB (200nM), biological rep2


title: Day 14 OS17 met

description: OS17 metastases collected at day 14

value: lung

value: Day 14


title: Pool_wt, biological rep3

value: Stage 40

value: not determined

value: wild type


title: Differentiated Brown adipocyte, DMSO, Day 7 Rep3

value: DMSO treated O/N


title: A375-BIR_DMSO #Crt_3

description: SmallTranscriptome profile of A375-BIR treated with DMSO (0.1%), biological rep3

value: DMSO


title: Pool_wt, biological rep2

value: embryo


title: Lung, cattle rep3, scRNAseq

description: 10× Genomics

organism: Bos taurus


title: A375-BIR_DMSO #Crt_2

description: SmallTranscriptome profile of A375-BIR treated with DMSO (0.1%), biological rep2


title: Differentiated Brown adipocyte, DMSO, Day7 Rep1

value: Immotalized pre brown adipocyte


title: Pool_wt, biological rep1


title: Differentiated Brown adipocyte, DMSO, Day 7 Rep2


title: A375_DMSO #_Crt_1

description: SmallTranscriptome profile of A375 treated with DMSO (0.1%), biological rep1


title: Lung, cattle rep2, scRNAseq

description: 10× Genomics


title: wt_D25_rep4

status: Public on May 02 2024

first: Bogdan

last: Sieriebriennikov

address: 100 Washington Sq E

institute: New York University

data_processing:
Mapping and counting was done using STAR v2.6.1d.
Count normalization was done using DESeq2 v1.34.0.
Assembly: Hsal_v8.6
Supplementary files format and content: tab-delimited text files that contain raw counts for each sample
Supplementary files format and content: comma-delimited text file that contains DESeq2-normalized counts for all samples

organism: Harpegnathos saltator

source_name: antenna

extract_protocol:
Antennae were frozen with liquid nitrogen and ground into a fine dry powder using a pestle. RNA was extracted via a standard protocol using TRIzol Reagent, followed by ethanol precipitation. DNase treatment was performed in-solution, followed by a second round of TRIzol-chloroform and ethanol precipitation to remove the treatment.
We used the NEBNext Ultra II RNA Library Prep Kit for Illumina with an input of 110 ng RNA and 12 PCR cycles.

value: antenna

value: wt

tag: sequencing batch

tag: time apf


title: Lung, cattle rep1, scRNAseq

description: 10× Genomics


title: mut_D15_rep2


title: wt_D15_rep4


title: mut_D25_rep2


title: mut_D25_rep3


title: mut_D25_rep1


title: Pool_ko, biological rep1

value: KO for SEDL


title: mut_D20_rep3


title: mut_D20_rep2


title: wt_lib_3

description: 10X Genomics, double-indexed, nuclei

data_processing:
Demultiplexing and counting were done using cellranger v7.0.0
Assembly: Hsal_v8.6
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

extract_protocol:
Antennae were frozen and ground with a pestle, then Dounce-homogenized in homogenization buffer (250 mM sucrose, 10 mM Tris pH 8.0, 25 mM KCl, 5 mM MgCl2, 0.1% Triton X-100, 0.5 mM RNAseOUT, 1X Promega protease inhibitor, 0.1 mM DTT), filtered, washed and resuspended in 1xPBS+1%BSA+1mM RNAseOUT, then filtered again
We used 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (single-index version for wt_lib_1 and dual-index version for the remaining libraries) and folllowed manufacturer's instructions.

tag: biological replicate


title: wt_lib_2

description: 10X Genomics, double-indexed, nuclei


title: wt_lib_1

description: 10X Genomics, single-indexed, nuclei


title: D27_3 HTO

city: Melbourne

first: Hyun Jae

last: Lee

address: 792 Elizabeth Street

department: Department of Microbiology and Immunology

country: Australia

institute: University of Melbourne

description:
10x Genomics
d27_3_barcodes.tsv.gz
d27_3_features.tsv.gz
d27_3_matrix.mtx.gz

data_processing:
Data was processed using the “cellranger multi” pipeline from Cell Ranger version 6.1.1 (10x Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Spleen

extract_protocol:
Polyclonal CD4+ T cells from spleens were isolated by flow cytometry into a 2% BSA/PBS buffer. For each timepoint, samples from each individual mouse replicate were labelled with a different hashtag reagent, and samples from 5 individual mouse replicates were pooled for isolating different populations of CD4+ T cells. At Day 30 and Day 3 after re-infection, CXCR3-/CD11a-low (marking naive cells) and CXCR3+/CD11a-high CD4+ T cells were sorted and pooled at a proportion of 1:9. Polyclonal CD4+ cells were sorted as single-cells using the Chromium 10x Genomics platform. Approximately 33,000 cells were loaded per channel onto a Chromium controller (10x Genomics) for generation of gel bead-in-emulsions using 10x Genomics Single Cell 5' Reagent Kit v2 (single-cell gene expression and immune repertoire profiling).
Sequencing libraries were prepared using Single Cell 5’ Reagent Kits v2 (10x Genomics) and then converted using the MGIEasy Universal Library Conversion Kit (BGI).

value: Spleen

tag: cell type

value: CD4-positive alpha-beta T cell

tag: strain

tag: age

value: 6-12 weeks


title: D30 HTO

description:
10x Genomics
d30_barcodes.tsv.gz
d30_features.tsv.gz
d30_matrix.mtx.gz


title: EEQ_3

city: Tianjin

first: Ting

last: Zhou

address: Qixiangtai road 22

institute: Tianjin medical university

data_processing:
Basecalls performed using BGISEQ-500
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using BWA.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: HUVECs

growth_protocol: HUVECs were cultured in M199 supplemented with 10%FBS and antibodies in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
HUVECs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using  oligo -dT beads

treatment_protocol: The cells were treated with 1 μM 17,18-EEQ for 24 hours until growth of 70% confluence

value: HUVECs

value: Endothelial cells

value: Wild type

tag: treatment


title: D30 GEX


title: A375-BIR_DMSO #Crt_1

description: SmallTranscriptome profile of A375-BIR treated with DMSO (0.1%), biological rep1


title: D30 TCR

description: 10x Genomics


title: D27_3 TCR

description: 10x Genomics


title: Control_3

value: PBS


title: wt_D20_rep4


title: mut_D15_rep3


title: EEQ_2


title: EEQ_1


title: Control_2